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Thinking process templates for constructing data stories with SCDNEY.

Yue Cao1,2,3,4, Andy Tran1,2,3,4, Hani Kim2,4,5

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Summary
This summary is machine-generated.

This study introduces scdney, a novel R package and living workshop series for single-cell data integration and analysis. These workshops facilitate accelerated scientific discovery by enabling cell phenotyping and disease progression prediction from complex biological data.

Keywords:
data analysisdata storyliving workshopsingle-cell analysisthinking process template

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Area of Science:

  • Biomedical Data Science
  • Computational Biology
  • Genomics

Background:

  • The biological sciences are experiencing a data revolution, generating vast high-throughput biomedical datasets.
  • Single-cell datasets are rapidly increasing, necessitating advanced analytical approaches.
  • Integrating diverse single-cell data is crucial for accelerating scientific discovery and clinical applications.

Purpose of the Study:

  • To present a novel framework for analyzing complex single-cell data.
  • To demonstrate efficient and purpose-specific data analysis strategies.
  • To foster collaborative learning in single-cell data science.

Main Methods:

  • Development of scdney, a wrapper package for single-cell analysis in R.
  • Implementation of 'living' workshops focused on data storytelling and analysis.
  • Utilizing R packages for data integration, cell type annotation, and higher-order testing.

Main Results:

  • Illustration of two workshops: one on cell phenotyping and relationships, another on predicting disease progression.
  • Demonstration of scdney's capabilities in handling complex single-cell datasets.
  • Showcasing current solutions and critical thinking points in single-cell data analysis.

Conclusions:

  • The 'living' workshop approach promotes collaborative learning and community contribution.
  • The Thinking Process Template offers a structured framework for single-cell data analysis decision-making.
  • scdney and associated workshops accelerate discovery by providing tailored, efficient analysis tools.